Version Information

This page presents a partial list of the data sources we download and integrate in our database. These data sources are created and maintained by groups other than ourselves, and we wish to thank these other groups for so generously providing their data to us and the rest of the scientific community.
The first section shows "datasets". Each dataset generally consist of many files which are released as a unit. The table shows the name of each dataset which is linked to the dataset's homepage, and the name or date of the release used in the current version of our database. In a few cases, no release name or date was available.
The second section shows the individual files that we download. The table indicates the full URL of each file, the date the file was updated by its maintainer, and the date we downloaded it. Note that the URL of the file is not hyperlinked, since clicking on such a link would cause the file to be downloaded to your computer which is probably not desirable. We have not grouped the files by data source since this is usually apparent from the URL.
The list of sources presented here is incomplete. Additional sources will be added in future releases.

Dataset Release
BioCarta (linked to genes using data from NCI Cancer Gene Anatomy Project) 19-Jan-2012
BioGRID Version 3.1.86, 25-Feb-2012
Database of Interacting Proteins (DIP) 28-Feb-2012
DoTS (Database Of Transcribed Sequences) human 21-Apr-2008
mouse 21-Apr-2008
Ensembl Release 66, Feb-2012
Gene Ontology Consortium Version 1.1.2689, 07-Mar-2012
Genetic Association Database 01-Aug-2011
HUGO Gene Nomenclature Committee 08-Mar-2012
Human Protein Reference Database (HPRD) Release 9, 13-Apr-2010
InParanoid: Eukaryotic Ortholog Groups Version 7.0, 28-Jun-2009
IntAct 07-Feb-2012
KEGG: Kyoto Encyclopedia of Genes and Genomes Release 58.1, 01-Jun-2011
MINT: a Molecular INTeraction database BINARY 2.6, 06-Feb-2012
Mouse Genome Informatics (MGI), Jackson Laboratory 07-Mar-2012
NCBI Entrez Gene 08-Mar-2012
NCBI HomoloGene Release 65, 14-Feb-2011
NCBI UniGene human Build #231, 21-Dec-2011
mouse Build #192, 20-Oct-2011
rat Build #191, 18-Jan-2012
OMIM, Online Mendelian Inheritance in Man 13-Mar-2012
OrthoMCL Version 5.0, 31-Mar-2011
PeptideAtlas Nov-2011
Rat Genome Database Version 2.1.2.1, 02-Mar-2012
Reactome - a curated knowledgebase of biological pathways Version 39, 14-Dec-2011
Sanger Interaction Map 13-Aug-2004
STRING (Search Tool for the Retrieval of Interacting Genes/Proteins) Version 9.0, 08-Mar-2012
The MIPS Mammalian Protein-Protein Interaction Database 08-Mar-2012
UCSC Genome Bioinformatics (Golden Path) human UCSC hg19, GRC build h37, Feb-2009
mouse UCSC mm9, NCBI Build 37.1, July-2007
rat UCSC rn4, RGSC version 3.4, Nov-2004
UniProt (Universal Protein Resource) Release 2012_02, 22-Feb-2012

File Update Date Download Date
ftp://ftp.ebi.ac.uk/pub/databases/intact/current/psimitab/intact.zip 09-Feb-2012 08-Mar-2012
ftp://ftp.ensembl.org/pub/current_mysql/ensembl_mart_66/hsapiens_gene_ensembl__homolog_mmus__dm.txt.gz 17-Feb-2012 08-Mar-2012
ftp://ftp.ensembl.org/pub/current_mysql/ensembl_mart_66/hsapiens_gene_ensembl__homolog_rnor__dm.txt.gz 17-Feb-2012 08-Mar-2012
ftp://ftp.ensembl.org/pub/current_mysql/ensembl_mart_66/mmusculus_gene_ensembl__homolog_hsap__dm.txt.gz 17-Feb-2012 08-Mar-2012
ftp://ftp.ensembl.org/pub/current_mysql/ensembl_mart_66/mmusculus_gene_ensembl__homolog_rnor__dm.txt.gz 17-Feb-2012 08-Mar-2012
ftp://ftp.ensembl.org/pub/current_mysql/ensembl_mart_66/rnorvegicus_gene_ensembl__homolog_hsap__dm.txt.gz 17-Feb-2012 08-Mar-2012
ftp://ftp.ensembl.org/pub/current_mysql/ensembl_mart_66/rnorvegicus_gene_ensembl__homolog_mmus__dm.txt.gz 17-Feb-2012 08-Mar-2012
ftp://ftp.expasy.org/databases/enzyme/enzyme.dat 18-Feb-2012 08-Mar-2012
ftp://ftp.geneontology.org/pub/go/ontology/gene_ontology.obo 08-Mar-2012 08-Mar-2012
ftp://ftp.genome.ad.jp/pub/kegg/genes/ko/ko 12-Jun-2011 13-Jun-2011
ftp://ftp.genome.ad.jp/pub/kegg/genes/organisms/hsa/hsa_ko.list 12-Jun-2011 13-Jun-2011
ftp://ftp.genome.ad.jp/pub/kegg/genes/organisms/hsa/hsa_ncbi-geneid.list 12-Jun-2011 13-Jun-2011
ftp://ftp.genome.ad.jp/pub/kegg/genes/organisms/hsa/hsa_pathway.list 12-Jun-2011 13-Jun-2011
ftp://ftp.genome.ad.jp/pub/kegg/genes/organisms/mmu/mmu_ko.list 12-Jun-2011 13-Jun-2011
ftp://ftp.genome.ad.jp/pub/kegg/genes/organisms/mmu/mmu_ncbi-geneid.list 12-Jun-2011 13-Jun-2011
ftp://ftp.genome.ad.jp/pub/kegg/genes/organisms/mmu/mmu_pathway.list 12-Jun-2011 13-Jun-2011
ftp://ftp.genome.ad.jp/pub/kegg/genes/organisms/rno/rno_ko.list 12-Jun-2011 13-Jun-2011
ftp://ftp.genome.ad.jp/pub/kegg/genes/organisms/rno/rno_ncbi-geneid.list 12-Jun-2011 13-Jun-2011
ftp://ftp.genome.ad.jp/pub/kegg/genes/organisms/rno/rno_pathway.list 12-Jun-2011 13-Jun-2011
ftp://ftp.genome.ad.jp/pub/kegg/pathway/map_title.tab 12-Jun-2011 13-Jun-2011
ftp://ftp.informatics.jax.org/pub/reports/HMD_Human1.rpt 07-Mar-2012 08-Mar-2012
ftp://ftp.informatics.jax.org/pub/reports/HMD_Human2.rpt 07-Mar-2012 08-Mar-2012
ftp://ftp.informatics.jax.org/pub/reports/HMD_Human3.rpt 07-Mar-2012 08-Mar-2012
ftp://ftp.informatics.jax.org/pub/reports/HMD_Human4.rpt 07-Mar-2012 08-Mar-2012
ftp://ftp.informatics.jax.org/pub/reports/HMD_Rat1.rpt 07-Mar-2012 08-Mar-2012
ftp://ftp.informatics.jax.org/pub/reports/HMD_Rat2.rpt 07-Mar-2012 08-Mar-2012
ftp://ftp.informatics.jax.org/pub/reports/HMD_Rat3.rpt 07-Mar-2012 08-Mar-2012
ftp://ftp.informatics.jax.org/pub/reports/HMD_Rat4.rpt 07-Mar-2012 08-Mar-2012
ftp://ftp.informatics.jax.org/pub/reports/HMD_RatHuman1.rpt 07-Mar-2012 08-Mar-2012
ftp://ftp.informatics.jax.org/pub/reports/HMD_RatHuman2.rpt 07-Mar-2012 08-Mar-2012
ftp://ftp.informatics.jax.org/pub/reports/HMD_RatHuman3.rpt 07-Mar-2012 08-Mar-2012
ftp://ftp.informatics.jax.org/pub/reports/HMD_RatHuman4.rpt 07-Mar-2012 08-Mar-2012
ftp://ftp.informatics.jax.org/pub/reports/MGI_EntrezGene.rpt 07-Mar-2012 08-Mar-2012
ftp://ftp.ncbi.nih.gov/gene/DATA/gene2accession.gz 07-Mar-2012 08-Mar-2012
ftp://ftp.ncbi.nih.gov/gene/DATA/gene2go.gz 07-Mar-2012 08-Mar-2012
ftp://ftp.ncbi.nih.gov/gene/DATA/gene2pubmed.gz 07-Mar-2012 08-Mar-2012
ftp://ftp.ncbi.nih.gov/gene/DATA/gene2refseq.gz 07-Mar-2012 08-Mar-2012
ftp://ftp.ncbi.nih.gov/gene/DATA/gene2unigene 08-Mar-2012 08-Mar-2012
ftp://ftp.ncbi.nih.gov/gene/DATA/gene_history.gz 07-Mar-2012 08-Mar-2012
ftp://ftp.ncbi.nih.gov/gene/DATA/gene_info.gz 07-Mar-2012 08-Mar-2012
ftp://ftp.ncbi.nih.gov/gene/DATA/mim2gene 08-Mar-2012 08-Mar-2012
ftp://ftp.ncbi.nih.gov/gene/DATA/README 21-Nov-2011 08-Mar-2012
ftp://ftp.ncbi.nih.gov/pub/HomoloGene/current/homologene.data 15-Feb-2011 08-Mar-2012
ftp://ftp.ncbi.nih.gov/repository/UniGene/Homo_sapiens/Hs.data.gz 18-Jan-2012 08-Mar-2012
ftp://ftp.ncbi.nih.gov/repository/UniGene/Homo_sapiens/Hs.retired.lst.gz 18-Jan-2012 08-Mar-2012
ftp://ftp.ncbi.nih.gov/repository/UniGene/Mus_musculus/Mm.data.gz 05-Mar-2012 08-Mar-2012
ftp://ftp.ncbi.nih.gov/repository/UniGene/Mus_musculus/Mm.retired.lst.gz 05-Mar-2012 08-Mar-2012
ftp://ftp.ncbi.nih.gov/repository/UniGene/Rattus_norvegicus/Rn.data.gz 02-Mar-2012 08-Mar-2012
ftp://ftp.ncbi.nih.gov/repository/UniGene/Rattus_norvegicus/Rn.retired.lst.gz 02-Mar-2012 08-Mar-2012
ftp://ftp.ncbi.nlm.nih.gov/pub/CCDS/current_human 07-Sep-2011 08-Mar-2012
ftp://ftp.ncbi.nlm.nih.gov/pub/CCDS/current_mouse 24-Jan-2011 08-Mar-2012
ftp://ftp.sanger.ac.uk/pub/CGP/cosmic/data_export/CosmicHGNC_v57_180112.tsv 18-Jan-2012 08-Mar-2012
ftp://ftp.sanger.ac.uk/pub/postgenomics/signaltransduction/interactionmap/complete.txt.gz 26-Apr-2004 08-Mar-2012
ftp://ftp.sanger.ac.uk/pub/postgenomics/signaltransduction/interactionmap/core.txt.gz 26-Apr-2004 08-Mar-2012
ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.dat.gz 22-Feb-2012 08-Mar-2012
ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_trembl.dat.gz 22-Feb-2012 08-Mar-2012
ftp://ftp1.nci.nih.gov/pub/CGAP/Hs_GeneData.dat 19-Jan-2012 08-Mar-2012
ftp://ftp1.nci.nih.gov/pub/CGAP/Mm_GeneData.dat 06-Mar-2012 08-Mar-2012
ftp://ftp1.nci.nih.gov/pub/PID/uniprot/uniprot.tab.gz 12-Jan-2012 08-Mar-2012
ftp://grcf.jhmi.edu/OMIM/omim.txt.Z 13-Mar-2012 13-Mar-2012
ftp://hgdownload.cse.ucsc.edu/goldenPath/currentGenomes/Mus_musculus/database/chromInfo.txt.gz 07-Mar-2012 08-Mar-2012
ftp://hgdownload.cse.ucsc.edu/goldenPath/currentGenomes/Rattus_norvegicus/database/chromInfo.txt.gz 21-Jun-2006 08-Mar-2012
ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/chromInfo.txt.gz 27-Apr-2009 08-Mar-2012
ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/cytoBand.txt.gz 14-Jun-2009 08-Mar-2012
ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/knownToLocusLink.txt.gz 05-Feb-2012 08-Mar-2012
ftp://hgdownload.cse.ucsc.edu/goldenPath/mm9/database/cytoBand.txt.gz 22-Aug-2007 08-Mar-2012
ftp://hgdownload.cse.ucsc.edu/goldenPath/mm9/database/knownToLocusLink.txt.gz 30-May-2011 08-Mar-2012
ftp://hgdownload.cse.ucsc.edu/goldenPath/rn4/database/cytoBand.txt.gz 21-Jun-2006 08-Mar-2012
ftp://hgdownload.cse.ucsc.edu/goldenPath/rn4/database/rgdGene2ToLocusLink.txt.gz 26-Feb-2012 08-Mar-2012
ftp://mint.bio.uniroma2.it/pub/release/mitab26/current/2012-02-06-mint-Mammalia-binary.mitab26.txt 06-Feb-2012 08-Mar-2012
ftp://rgd.mcw.edu/pub/data_release/GENES_HUMAN.txt 03-Mar-2012 08-Mar-2012
ftp://rgd.mcw.edu/pub/data_release/GENES_MOUSE.txt 03-Mar-2012 08-Mar-2012
ftp://rgd.mcw.edu/pub/data_release/GENES_RAT.txt 03-Mar-2012 08-Mar-2012
ftp://rgd.mcw.edu/pub/data_release/RGD_ORTHOLOGS 28-Sep-2011 08-Mar-2012
http://banon.cshl.edu:5555/biomart/martservice 11-Oct-2011 08-Mar-2012
http://dip.doe-mbi.ucla.edu/dip/Download.cgi 28-Feb-2012 08-Mar-2012
http://geneticassociationdb.nih.gov/all.xls 06-Jul-2006 08-Mar-2012
http://inparanoid.sbc.su.se/download/current/table_stats/InParanoid.H.sapiens-M.musculus 29-Apr-2009 08-Mar-2012
http://inparanoid.sbc.su.se/download/current/table_stats/InParanoid.H.sapiens-R.norvegicus 29-Apr-2009 08-Mar-2012
http://inparanoid.sbc.su.se/download/current/table_stats/InParanoid.M.musculus-R.norvegicus 29-Apr-2009 08-Mar-2012
http://mips.gsf.de/proj/ppi/data/mppi.gz 01-Jun-2004 08-Mar-2012
http://string.embl.de/newstring_download/protein.links.detailed.v9.0.txt.gz 28-May-2011 08-Mar-2012
http://string.embl.de/newstring_download/protein.links.v9.0.txt.gz 29-May-2011 08-Mar-2012
http://thebiogrid.org/downloads/archives/Release%20Archive/BIOGRID-3.1.86/BIOGRID-ALL-3.1.86.tab.zip 25-Feb-2012 08-Mar-2012
http://www.cbil.upenn.edu/downloads/DoTS/current_human/humDoTS_DTToGeneId.dat.gz 10-Mar-2008 06-Oct-2011
http://www.cbil.upenn.edu/downloads/DoTS/current_mouse/musDoTS_DTToGeneId.dat.gz 06-Apr-2007 06-Oct-2011
http://www.genenames.org/cgi-bin/hgnc_downloads.cgi 08-Mar-2012 08-Mar-2012
http://www.hprd.org/download/HPRD_Release_9_041310.txt.gz 13-Apr-2010 08-Mar-2012
http://www.orthomcl.org/common/downloads/release-5/groups_OrthoMCL-5.txt.gz 15-Apr-2011 08-Mar-2012
http://www.peptideatlas.org/builds/human/201111/APD_ensembl_hits.tsv 16-Nov-2011 08-Mar-2012
http://www.peptideatlas.org/builds/human/plasma/201005/APD_ensembl_hits.tsv 27-Oct-2010 08-Mar-2012
http://www.reactome.org/download/current/homo_sapiens.interactions.txt.gz 09-Dec-2011 08-Mar-2012